Hi All,
I am facing a weird problem while calculating the rmsd using
ptraj. I am doing the canonical simulation of TrpCage miniprotein at
325k. I followed the steps available online (provided by ross
Walker ). After heating the system to the desired temperature, I
created a pdb file and it looks reasonable. Then I performed 100ps
short canonical MD at this temperature and stored the configuration
in every 50 steps (ntwx=50). While I calculated the rmsd of the
trajectory from the experimental nmr structure, I found that 3rd &
4th snapshots give absurd rmsd (300+ AA). If I make ntwx=1, still I
found that 3rd & 4th snapshots gives absurd rmsd.
Below is my input file for canonical MD simulation: